James H. Walker ,  Kejia Yan ,  Ratmir Derda

Biochemistry

DOI: 10.1021/acs.biochem.5c00646

Abstract

Peptide-derived macrocycles are an emerging class of therapeutics capable of modulating protein–protein interactions that remain inaccessible to small molecules. Genetically encoded library (GEL) platforms such as phage and mRNA display have accelerated macrocyclic ligand discovery by linking peptide sequence to genotype and enabling selections from libraries with up to 10¹³ members. Efforts to expand the chemical space of GELs have included incorporation of electrophiles, either to generate libraries of true covalent ligands or to enable intramolecular reactions such as peptide cyclization. In the latter case, the electrophile is consumed during library construction, producing transient covalent libraries that enhance stability and diversity but are not designed for direct covalent engagement with targets. By contrast, recent advances have established robust strategies for embedding persistent electrophilic warheads that remain intact during library preparation and selectively react with nucleophilic residues on proteins. These approaches have yielded both reversible and irreversible covalent inhibitors against diverse classes of proteins, while also highlighting challenges in balancing electrophile reactivity with library integrity. Complementary developments in DNA-encoded covalent libraries further underscore the breadth of discovery platforms, though genetically encoded approaches remain uniquely powerful for macrocyclic peptides. Together, these advances define the trajectory of covalent genetically encoded libraries (cGELs) and point toward new opportunities for discovering ligands to historically undruggable targets.